GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Caulobacter vibrioides NA1000; Escherichia coli str. K-12 substr. MG1655; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL27158 GPL26592 GPL34253

20 Samples

Download data: TXT, XLSX

(Submitter supplied) In contrast to mammalian cells, bacterial cells lack mRNA polyadenylated tails, presenting a hurdle in isolating mRNA amidst the prevalent rRNA during single-cell RNA-seq. This study introduces a novel method, Ribosomal RNA-derived cDNA Depletion (RiboD), seamlessly integrated into the PETRI-seq technique, yielding RiboD-PETRI. This innovative approach offers a cost-effective, equipment-free, and high-throughput solution for bacterial single-cell RNA sequencing (scRNA-seq). more...

Organism:

Escherichia coli str. K-12 substr. MG1655; Caulobacter vibrioides NA1000; Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34253 GPL26592 GPL27158

19 Samples

Download data: TXT, XLSX

(Submitter supplied) Gene expression profile of the Streptococcus sanguinis comC deletion mutant compared to the wild-type strain SK36

Organism:

Streptococcus sanguinis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22689

8 Samples

Download data: TXT

(Submitter supplied) Cyclic di-AMP is an essential and ubiquitous second messenger that regulates bacterial potassium (K+) concentrations to maintain osmotic equilibrium. And its specific K+ regulation mechanism in Mycoplasma has rarely been investigated. We used the ruminant pathogen Mycoplasma bovis (M. bovis) to investigate this mechanism. We verified that MbovP496 is a c-di-AMP synthetase and its mutant T5.415 showed growth inhibition under high K+ condition. more...

Organism:

Mycoplasmopsis bovis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34563

12 Samples

Download data: TXT

(Submitter supplied) We used culturing of fecal sample enrichments on solid medium containing gastric mucin as the main carbon source to isolate a novel bacterium that is largely restricted to using the N-acetylglucosamine and N-acetylgalactosamine sugars from mucin. This butyrate-producing bacterium accesses these sugars from both polymeric gastric mucin and chemically released oligosaccharides and has a genome with correspondingly restricted carbohydrate-active enzyme content. more...

Organism:

Erysipelotrichaceae bacterium DSM 116809

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34484

15 Samples

Download data: GFF, XLSX

(Submitter supplied) Paenarthrobacter nicotinovorans pAO1 is a nicotine degrading microorganism that shows promising applications in converting nicotine-containing waste into useful green chemicals. Its biotechnological applications are nevertheless hampered by the lack of knowledge and tools to perform genetic and metabolic engineering. The objective of the work is to provide the first transcriptome of the strain and is a second step in our envisioned complete omics characterization of nicotine metabolism in P. more...

Organism:

Paenarthrobacter nicotinovorans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33653

15 Samples

Download data: GTF, TXT

(Submitter supplied) Sodium oligomannate (GV-971), an oligosaccharide drug approved in China for treating mild-to-moderate Alzheimer's disease (AD), was previously found to recondition the gut microbiota and limit altered peripheral Th1 immunity in AD transgenic mice. As a follow-up study, we here provide advances by pinpointing a Lactobacillus murinus strain that highly expressed a gene encoding a putative adhesin containing Rib repeats (Ribhigh-L.m.) that was particularly enriched in 5XFAD transgenic mice. more...

Organism:

Ligilactobacillus murinus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33917

6 Samples

Download data: CSV

(Submitter supplied) To investigate the subspecies level differences in the expression profiles of Streptococcus salivarius strains, we conducted the RNA sequencing analysis of Streptococcus salivarius strains.

Organism:

Streptococcus salivarius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34965

24 Samples

Download data: TXT

(Submitter supplied) We found that biofilm formation ability of E. faecalis was impacted by surfactin. To further understand how E. faecalis responded to surfactin, we searched for differentially expressed genes between E. faecalis treated with or without surfactin using RNA-seq analysis.

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35064

2 Samples

Download data: XLSX

(Submitter supplied) Deletion of the global transcription factor PacR in Anabaena triggers heterocyst formation even in NO3- containing medium, likely due to impaired NO3- uptake and disrupted NH4+ assimilation in the GOGAT cycle. This phenotype may be exacerbated by reduced PSI-yield and reduced expression of ferredoxin, which may lead to less reducing equivalents for nitrogen uptake and fixation. These results highlight PacR’s role as a global regulator of carbon metabolism and photosynthesis while also establishing its involvement in regulating nitrogen metabolism.

Organism:

Nostoc sp. PCC 7120 = FACHB-418

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35023

18 Samples

Download data: TXT

(Submitter supplied) Biofilm formation is an important mechanism of survival and persistence for many bacterial pathogens. These multicellular communities contain subpopulations of cells that display vast metabolic and transcriptional diversity along with high recalcitrance to antibiotics and host immune defenses. Investigating the complex heterogeneity within biofilm has been hindered by the lack of a sensitive and high-throughput method to assess stochastic transcriptional activity and regulation between bacterial subpopulations, which requires single-cell resolution. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28116

2 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL25368 GPL28679 GPL29157

26 Samples

Download data

(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Streptococcus agalactiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29157

18 Samples

Download data: TXT

(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other

Platforms:

GPL28679 GPL25368

8 Samples

Download data: XLSX

(Submitter supplied) Mycobacterium tuberculosis can use a proteasome to degrade proteins when they are post-translationally modified with prokaryotic ubiquitin-like protein (Pup). While pupylation is reversible, mechanisms regulating depupylation have not been identified. Here, we identify a depupylation regulator, CoaX, a pseudo-pantothenate kinase. Pantothenate synthesis enzymes were more abundant in a ∆coaX mutant, including PanB, a substrate of the Pup-proteasome system. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27507

12 Samples

Download data: TSV

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. Hence, the characterization of new RNA families with deep sequence and/or structure conservation has the potential to reveal new molecular and biological RNA functions. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25258

12 Samples

Download data: WIG

(Submitter supplied) Bacterial non-coding RNAs fulfill a variety of cellular functions, for example as catalysts of chemical reactions, as structural components in multiprotein complexes or as regulators of gene expression at the transcriptional and post-transcriptional level. Some RNAs, such as ribosomal RNAs, display exceptionally broad conservation across bacterial phyla and are involved in fundamental and unique cellular functions. more...

Organism:

Clostridioides difficile

Type:

Other

Platform:

GPL30071

28 Samples

Download data: RC, XML

(Submitter supplied) Group A Streptococcus (GAS) is a human-adapted pathogen responsible for a variety of diseases. The GAS M1UK lineage has contributed significantly to the recently reported increases in scarlet fever and invasive infections, however the basis for its evolutionary success is not yet fully understood. During the transition to systemic disease, the M1 serotype is known to give rise to spontaneous mutations in the CovRS two-component transcriptional regulation system that confer a fitness advantage during invasive infections. more...

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28678

12 Samples

Download data: TSV

(Submitter supplied) Single-molecule correlated chemical probing (smCCP) is an experimentally concise strategy for characterizing higher-order structural interactions in RNA. smCCP data yield rich, but complex, structural information on base pairing, conformational ensembles, and tertiary interactions. To date, through-space communication specifically measuring RNA tertiary structure has been difficult to isolate from structural communication reflective of other interactions. more...

Organism:

Enterococcus faecalis

Type:

Other

Platform:

GPL24867

15 Samples

Download data

(Submitter supplied) Tuberculosis (TB) is one of the leading causes of death due to a single infectious agent and is considered a global threat killing over 4,300 people every day. Upon infection, Mycobacterium tuberculosis (M.tb) deposits in the alveoli and encounters the lung mucosa or alveolar lining fluid (ALF), whose primary function is to keep the lung’s health intact, dictating host-cell interactions. Age-associated changes to innate soluble components in the ALF lead to increased susceptibility of the elderly population to respiratory infectious diseases such as TB. more...

Organism:

Mycobacterium tuberculosis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22688

14 Samples

Download data: TXT